9G1R | pdb_00009g1r

Fragment screening of FosAKP, cryo structure in complex with fragment F2X-entry G12

• PDB DOI: https://doi.org/10.2210/pdb9G1R/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-10 Released: 2025-07-23 
• Deposition Author(s): Guenther, S., Galchenkova, M., Fischer, P., Reinke, P.Y.A., Falke, S., Thekku Veedu, S., Rodrigues, A.C., Senst, J., Meents, A.
• Funding Organization(s): German Federal Ministry for Education and Research, Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Room temperature X-ray fragment screening with serial crystallography

Guenther, S., Meents, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.18 kDa 
• Atom Count: 2,827 
• Modeled Residue Count: 275 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fosfomycin resistance protein	A, B	145	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: KPNJ1_04856

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SZ7 (Subject of Investigation/LOI)	D [auth A], F [auth B]	~{N}-[(~{E})-thiophen-2-ylmethylideneamino]cyclopropanecarboxamide C9 H10 N2 O S WQCIBERJKZYXCC-UXBLZVDNSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.789	α = 90
b = 89.623	β = 90
c = 44.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
autoPROC	data processing
Coot	model building
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Guenther, S., Galchenkova, M., Fischer, P., Reinke, P.Y.A., Falke, S., Thekku Veedu, S., Rodrigues, A.C., Senst, J., Meents, A.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	16GW0277
German Federal Ministry for Education and Research	Germany	13K22CHB
Helmholtz Association	Germany	FISCOV
Helmholtz Association	Germany	SFragX
Helmholtz Association	Germany	HIR3X

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release